Beta diversity

From 16S rRNA-gene sequencing of cow milk microbiome samples: - 4 timepoints for milk samples and two treatments (oil, treated/untreated)

Between-sample variability from 16S rRna-gene sequencing data.

Clustering

PCA

Clustering by timepoint (PCA):

Clustering by treatment (PCA): after removing samples from timepoint 0 # BECAUSE WE KNOW THAT AT TIMEPOINT 0 WE SHOULD NOT HAVE DIFFERENCES BETWEEN GROUPS

Clustering by treatment (PCA): by timepoints

Time-point 28

## Warning in data.frame(..., check.names = FALSE): row names were found from a
## short variable and have been discarded

Time-point 21

## Warning in data.frame(..., check.names = FALSE): row names were found from a
## short variable and have been discarded

Time-point 8

## Warning in data.frame(..., check.names = FALSE): row names were found from a
## short variable and have been discarded

Time-point 0

## Warning in data.frame(..., check.names = FALSE): row names were found from a
## short variable and have been discarded

MDS

Clustering by treatment (MDS): NMDS1 vs NMDS2

Clustering by timepoint (MDS):

NMDS1 vs NMDS2

Clustering by type (MDS): NMDS1 vs NMDS3

Clustering by type (MDS): NMDS2 vs NMDS3

Clustering by treatment by timepoint (MDS):

Significance of between-group distances

Significance values based on permuted analysis of variance (999 permutations), repeated 100 times.

Below the ANOVA table from the model:

\[ X = \mu + treatment + timepoint + treatment*type + e \]

Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
treatment 1 0.3754833 0.3754833 1.702507 0.0256107 0.041
timepoint 3 1.2733871 0.4244624 1.924586 0.0868544 0.004
residuals 59 13.0122919 0.2205473 NA 0.8875348 NA
total 63 14.6611623 NA NA 1.0000000 NA

going 3D

## Run 0 stress 0.07511949 
## Run 1 stress 0.07982514 
## Run 2 stress 0.07979209 
## Run 3 stress 0.07508381 
## ... New best solution
## ... Procrustes: rmse 0.006178098  max resid 0.03090521 
## Run 4 stress 0.07511025 
## ... Procrustes: rmse 0.005230696  max resid 0.03103953 
## Run 5 stress 0.08117002 
## Run 6 stress 0.07511956 
## ... Procrustes: rmse 0.006163733  max resid 0.03118073 
## Run 7 stress 0.08845616 
## Run 8 stress 0.07508376 
## ... New best solution
## ... Procrustes: rmse 0.0001836155  max resid 0.0009432191 
## ... Similar to previous best
## Run 9 stress 0.09210695 
## Run 10 stress 0.07541573 
## ... Procrustes: rmse 0.01042587  max resid 0.06485814 
## Run 11 stress 0.08579224 
## Run 12 stress 0.07510211 
## ... Procrustes: rmse 0.003036263  max resid 0.0197986 
## Run 13 stress 0.07979847 
## Run 14 stress 0.07511062 
## ... Procrustes: rmse 0.005221525  max resid 0.03095948 
## Run 15 stress 0.08233311 
## Run 16 stress 0.08879875 
## Run 17 stress 0.08829215 
## Run 18 stress 0.07511165 
## ... Procrustes: rmse 0.005246247  max resid 0.03101884 
## Run 19 stress 0.07508407 
## ... Procrustes: rmse 0.0001698039  max resid 0.00101293 
## ... Similar to previous best
## Run 20 stress 0.07512631 
## ... Procrustes: rmse 0.005689686  max resid 0.03113833 
## *** Solution reached

timepoint 0

timepoint 8

timepoint 21

timepoint 28